Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
MOLM-13
Primary Tissue
Blood
Tissue Diagnosis
Leukemia Acute Myelogenous

Attributes by original data submitter

Sample

source_name
peripheral blood
cell line
MOLM13 leukemia cells
cell type
Human-derived acute myeloid leukemia
tissue
peripheral blood
disease state
acute myeloid leukemia
chip antibody
Cell Signaling Technology, Cat# 2899
genotype
WT

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
RNA samples extracted with Trizon and treated with Dnase I. ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF, SA1, SA2, RAD21, H3K4me3 and H3K27me3 antibody (antibody: Anti-CTCF, Cell Signaling Technology, Cat# 2899; Anti-SA1, Abcam, Cat# ab4457; Anti-SA2, Abcam, Cat# ab4464; Anti-RAD21, Abcam, Cat# ab992; Anti-H3K4me3, Millipore, Cat No. 04-745; Anti-H3K27me3, Millipore, Cat No. 07-449). ATAC-seq samples derived according to Nextera Tn5 Transposase kits. DNA:RNA immunoprecipitation sequencing (DRIP-seq) was performed as described previously with s9.6 antibody (Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001). NG-Capture-C assay was performed as previously described. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications. Single cells were generated using Chromium Controller (10x Genomics), and scRNA-seq and scATAC-seq libraries were constructed using chromium single cell 3' reagent kits v2 (10x Genomics, California USA) according to the manufacturer's recommendations. RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594). ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). NG-Capture-C-seq libraries were prepared according to using the Herculase II PCR kit (Agilent). . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg38

Number of total reads
65540773
Reads aligned (%)
97.0
Duplicates removed (%)
8.0
Number of peaks
21959 (qval < 1E-05)

hg19

Number of total reads
65540773
Reads aligned (%)
96.1
Duplicates removed (%)
8.4
Number of peaks
20749 (qval < 1E-05)

Base call quality data from DBCLS SRA